What does the 12 volt battery do that the big battery can't? Surely it wouldn't be difficult to tap 12 volts off the main pack.
Lights? Windshield wipers? Horn? Radio and touchscreen? All things the big battery can easily supply power for.
This is an easy one, the big battery powers 2 things in the car, the motor, the AC. (okay, maybe 2.5, also the 12V charger)
The 12V batter runs everything else, the computers, the lights, wipers, the 12V plug, headlamps and a bunch of others.
You can not get rid of the 12V, it has to exist for at least the 12V plug. And when you look at "low cost" parts, that means mass production and all parts are generally 12V.
Now, I believe that Elon has mentioned that he wants to increase the distribution voltage, to something like 48V, but that tends to suggest that a lot of down-converters will be needed all over the car. LEDs don't run at 48V, but then again, they don't run at 12V, so it is a different converter needed.
48V means that smaller wires will be needed and possibly less wires because larger buss wires can be used.
But just about everything in the car is 12V today, so that 12V battery is pretty crucial to operation. Heck, both the Bluetooth and card key mechanisms are coming off the 12V battery, so it is quite essential.